Microsatellite markers for the Indian golden silkmoth, Antheraea assama (Saturniidae: Lepidoptera)

Antheraea assama, an economically important and scientifically unexplored Indian wild silkmoth, is unique among saturniid moths. For this species, a total of 87 microsatellite markers was derived from 35 000 expressed sequence tags and a microsatellite‐enriched sub‐genomic library. Forty individuals collected from Tura and West Garo Hills region of Northeast India were screened for each of these loci. Ten loci from expressed sequence tags and one from genomic library were found to be polymorphic. These microsatellite markers will be useful resources for population genetic studies of A. assama and other closely related species of saturniids. This is the first report on development of microsatellite markers for any saturniid species.     

羚牛的遗传多样性及其种群遗传结构分析

羚牛是亚洲大陆一种特有的大型珍稀动物,目前正面临着栖息地丧失、片段化和人类活动的严重威胁。为了有效地保护这种濒危动物,全面了解羚牛的种群结构、进化历史和整个分布区内遗传多样性的分布是至关重要的。本研究以mtDNA D-loop330bp基因片段为分子标记,比较分析了来自陕西秦岭、甘肃南部、四川岷山、邛崃山和云南贡山的40个样品的序列差异,根据分布特点将所采集到的羚牛分为3个地理单元,即秦岭、四川和云南。结果表明,在3个地理单元中存在4种单倍型,且地理单元间不存在共享单倍型,相互单倍型之间的平均序列差异为1.66％。进一步分析表明,3个地理单元间的基因流较低,存在着显的遗传分化 ,说明羚牛具有明显的系统地理分布格局。同时提出应将分布于秦岭山区、唐家河青川地区、天全以及云南贡山地区作为独立的管理单元分别加以保护。     

Genetic Diversity and Population Structure of Alnus hirsuta (Betulaceae) in Korea

Alnus hirsuta in Korea was measured to estimate the amount and pattern of genetic diversity and population structure. The mean genetic diversity within populations was 0.166. Korean alder populations have slightly high levels of genetic diversity compared to those of two Canadian alder species. The genetic differentiation among populations accounted for 9% of the total variation. The rate of gene flow was estimated high (Nm=2.63). Analysis of inbreeding coefficient, calculated for all polymorphic loci in each population, showed a substantial heterozygote deficiency relative to Hardy-Weinberg expectations. The mean G _ST value of A. hirsuta in Korea was 0.087. The low value of G _ST in this species, reflecting little spatial genetic differentiation, may indicate extensive gene flow. A relationship between the mean heterozygosity and annual rainfall showed a positive relationship (r ²=0.54, F=4.67). Received 8 August 1998/ Accepted in revised form 7 July 1999     

Genetic Diversity and Population Structure of Teucrium polium (Lamiaceae) in Tunisia

Random amplified polymorphic DNA markers were used to assess the genetic diversity within and among seven Tunisian diploid and polyploid populations of Teucrium polium L. from five bioclimatic areas. Out of the 141 bands generated from eight selected primers, 124 were polymorphic. The genetic diversity within a population (Shannon’s index) was high and varied according both the ploidal levels and bioclimatic zones. The genetic differentiation among populations assessed by G _ST and Φ_ST statistics was high, suggesting a low level of gene flow among them. The major proportion of the variation was attributable to individual differences within populations. The UPGMA analysis based on Nei and Li’s coefficient showed that individuals from each population clustered together. In a dendrogram using the Φ_ST distance matrix, population grouping is concordant with bioclimates and cytotypes. Conservation strategies should take into account the level of the genetic diversity of the populations according to their bioclimate and ploidal levels.     

Genetic Diversity and Population Structure of Juniperus rigida (Cupressaceae) and Juniperus coreana

Enzyme electrophoresis was used to estimate genetic diversity and population structure of Juniperus rigida (Cupressaceae) and Juniperus coreana in Korea. In J. rigida, 16 of the 22 loci (72.7%) showed detectable polymorphism. Genetic diversity (0.224) was higher than average values for species with similar life history traits. The endemic species (J. coreana) was found to have fewer alleles per locus (1.39 vs. 1.61), fewer alleles per polymorphic locus (2.42 vs. 2.63), lower percent polymorphic locus (54.6 vs. 72.7%), and lower diversity (0.199 vs. 0.224) than J. rigida. These genetic diversity parameters indicated that J. coreana was genetically depauperate relative to its presumptive progenitor, J. rigida. Analysis of fixation indices showed a substantial deficiency of heterozygotes relative to Hardy–Weinberg expectations suggesting inbreeding in J. coreana. The G _ST values of J. rigida and J. coreana were 0.173 and 0.118 respectively. The indirect estimate of gene flow based on mean G _ST was moderate (Nm = 1.19 for J. rigida and 1.86 for J. coreana). This revised version was published online in July 2006 with corrections to the Cover Date.     

独龙牛遗传多样性及其种群遗传结构的等位酶分析

采用水平片淀粉凝胶电泳技术,进行３０头独牛牛４１种蛋白质共计４４个遗传座位的等位酶分析,只在Ｔｒ,Ｈｐ,Ａｍｙ,Ｅｓｔ等４个座位发现多态性。每个座位等基因的平均数、多态座位百分比和平均杂合度值分别为Ａ＝１．０９０９、Ｐ＝０．０６８２和Ｈ＝０．０２６２。贡山县和福贡县独龙牛群体从酶基因的角度上看遗传多样性贫乏,可能是分别由小种群引种而来,受到瓶颈效应的作用,并伴随着创立者事件的发生。我们结合独龙牛在     

Genetic Diversity and Population Structure Analysis in Indian Mustard Germplasm Using Phenotypic Traits and SSR Markers

Plant Molecular Biology Reporter - Indian mustard is an economically important oilseed crop in India; therefore, exploring the genetic diversity of various germplasm collections is quite relevant...     

Genetic Diversity and Population Structure of Acacia senegal (L) Willd. in Kenya

The level of genetic diversity and population structure of Acacia senegal variety kerensis in Kenya was examined using seven polymorphic nuclear microsatellite loci and two chloroplast microsatellite loci. In both chloroplast and nuclear datasets, high levels of genetic diversity were found within all populations and genetic differentiation among populations was low, indicating extensive gene flow. Analysis of population structure provided support for the presence of two groups of populations, although all individuals had mixed ancestry. Groups reflected the influence of geography on gene flow, with one representing Rift Valley populations whilst the other represented populations from Eastern Kenya. The similarities between estimates derived from nuclear and chloroplast data suggest highly effective gene dispersal by both pollen and seed in this species, although population structure appears to have been influenced by distributional changes in the past. The few contrasts between the spatial patterns for nuclear and chloroplast data provided additional support for the idea that, having fragmented in the past, groups are now thoroughly mixed as a result of extensive gene flow. For the purposes of conservation and in situ management of genetic resources, sampling could target a few, large populations ideally distributed among the spatial groups identified. This should ensure the majority of extant variation is preserved, and facilitate the investigation of variation in important phenotypic traits and development of breeding populations.     

云杉矮槲寄生遗传多样性及其群体遗传结构分析

该研究采用CTAB法提取云杉矮槲寄生(Arceuthobium sichuanense)的基因组DNA,利用ITS1片段的序列信息对中国9个不同地理群体的62份云杉矮槲寄生样本的遗传多样性及群体遗传结构进行分析。结果表明:(1)62条ITS1序列共定义16个单倍型(H1~H16),表现出较低的遗传多样性水平(h=0.678 5,π=0.005 9),而群体间的遗传多样性水平则表现出较大差异(h=0~1.000 0,π=0~0.009 4);AMOVA分析显示云杉矮槲寄生群体内的遗传变异占到51.37%,群体间为48.63%。(2)Network单倍型网络分析表明,单倍型H1和H12较为古老,且所有群体对2种单倍型无共享现象;单倍型H1是广布单倍型,存在于青海和甘肃的6个群体中,单倍型H12仅在四川的2个群体中有分布。(3)基于最大似然法(ML)构建的群体聚类和中介邻接法构建的单倍型网络图均显示,四川的3个群体为独立类群,区别于青海、甘肃群体,且甘肃和青海的群体之间没有明显分化。该研究首次报道了云杉矮槲寄生遗传多样性和遗传结构,为进一步研究其进化及后续的病害防控提供了一定的参考。     

北沙柳群体遗传多样性和遗传结构分析

以内蒙古北沙柳(Salix psammophila)国家种质资源库内9个群体(P1~P9)288个无性系为实验材料,利用TP-M13-SSR技术,选取22对具有多态性EST-SSR北沙柳引物,采用毛细管电泳对PCR产物进行检测,分析北沙柳遗传多样性、分化程度和群体遗传结构,为北沙柳种质资源库遗传管理、无性系鉴定、品种选育、遗传改良和构建指纹图谱提供理论依据。结果显示:(1)22对EST-SSR引物共检测到222个等位基因,各位点平均等位基因数(A)为10,四倍体基因型丰富度(G)和特异基因型(G1)总和分别为1 460和802个,平均特异基因型比率(P1)和种质鉴别率(P2)分别为45.86%和13.21%。(2)9个群体平均等位基因数(A)为7.475,基因型丰富度(G)为15.586,观察杂合度(Ho)和期望杂合度(He)分别为0.577和0.638。以期望杂合度He为标准,北沙柳群体遗传多样性水平最低的是P1和P9。(3)北沙柳群体遗传分化系数仅为0.02,AMOVA分子变异分析显示,北沙柳群体大部分遗传变异来自群体内(97%),群体间变异仅为3%。(4)三维主成分、聚类和Structure群体遗传结构分析显示,9个群体被划分为2个组,Mantel检验表明北沙柳遗传距离与地理距离极显著相关(r=0.684 P0.001)。研究表明,北沙柳种质资源具有丰富的遗传多样性,这是其具有耐旱、耐寒、耐高温、耐沙埋和抗风蚀等适应性较强的分子基础;北沙柳的遗传变异集中在群体内;分布区群体呈现由中心向边缘群体扩张分化的趋势。     

Genetic Diversity and Population Structure of Cucumber (Cucumis sativus L.)

Knowing the extent and structure of genetic variation in germplasm collections is essential for the conservation and utilization of biodiversity in cultivated plants. Cucumber is the fourth most important vegetable crop worldwide and is a model system for other Cucurbitaceae, a family that also includes melon, watermelon, pumpkin and squash. Previous isozyme studies revealed a low genetic diversity in cucumber, but detailed insights into the crop''s genetic structure and diversity are largely missing. We have fingerprinted 3,342 accessions from the Chinese, Dutch and U.S. cucumber collections with 23 highly polymorphic Simple Sequence Repeat (SSR) markers evenly distributed in the genome. The data reveal three distinct populations, largely corresponding to three geographic regions. Population 1 corresponds to germplasm from China, except for the unique semi-wild landraces found in Xishuangbanna in Southwest China and East Asia; population 2 to Europe, America, and Central and West Asia; and population 3 to India and Xishuangbanna. Admixtures were also detected, reflecting hybridization and migration events between the populations. The genetic background of the Indian germplasm is heterogeneous, indicating that the Indian cucumbers maintain a large proportion of the genetic diversity and that only a small fraction was introduced to other parts of the world. Subsequently, we defined a core collection consisting of 115 accessions and capturing over 77% of the SSR alleles. Insight into the genetic structure of cucumber will help developing appropriate conservation strategies and provides a basis for population-level genome sequencing in cucumber.     

Population Structure and Genetic Diversity of Native and Invasive Populations of Solanum rostratum (Solanaceae)

Aims

We investigate native and introduced populations of Solanum rostratum, an annual, self-compatible plant that has been introduced around the globe. This study is the first to compare the genetic diversity of Solanum rostratum between native and introduced populations. We aim to (1) determine the level of genetic diversity across the studied regions; (2) explore the likely origins of invasive populations in China; and (3) investigate whether there is the evidence of multiple introductions into China.

Methods

We genotyped 329 individuals at 10 microsatellite loci to determine the levels of genetic diversity and to investigate population structure of native and introduced populations of S. rostratum. We studied five populations in each of three regions across two continents: Mexico, the U.S.A. and China.

Important Findings

We found the highest genetic diversity among Mexican populations of S. rostratum. Genetic diversity was significantly lower in Chinese and U.S.A. populations, but we found no regional difference in inbreeding coefficients (F _IS) or population differentiation (F _ST). Population structure analyses indicate that Chinese and U.S.A. populations are more closely related to each other than to sampled Mexican populations, revealing that introduced populations in China share an origin with the sampled U.S.A. populations. The distinctiveness between some introduced populations indicates multiple introductions of S. rostratum into China.     

Genetic Diversity and Population Structure in Western Hoolock (Hoolock hoolock) Gibbons in India

International Journal of Primatology - Geographic and anthropogenic barriers can result in creating population structure in primates. We hypothesized that such features in the Northeast India could...     

Genetic Diversity and Population Structure Analysis Between Indian Red Jungle Fowl and Domestic Chicken Using Microsatellite Markers

The present study was conducted to assess the genetic diversity, population structure, and relatedness in Indian red jungle fowl (RJF, Gallus gallus murgi) from northern India and three domestic chicken populations (gallus gallus domesticus), maintained at the institute farms, namely White Leghorn (WL), Aseel (AS) and Red Cornish (RC) using 25 microsatellite markers. All the markers were polymorphic, the number of alleles at each locus ranged from five (MCW0111) to forty-three (LEI0212) with an average number of 19 alleles per locus. Across all loci, the mean expected heterozygosity and polymorphic information content were 0.883 and 0.872, respectively. Population-specific alleles were found in each population. A UPGMA dendrogram based on shared allele distances clearly revealed two major clusters among the four populations; cluster I had genotypes from RJF and WL whereas cluster II had AS and RC genotypes. Furthermore, the estimation of population structure was performed to understand how genetic variation is partitioned within and among populations. The maximum ?K value was observed for K = 4 with four identified clusters. Furthermore, factorial analysis clearly showed four clustering; each cluster represented the four types of population used in the study. These results clearly, demonstrate the potential of microsatellite markers in elucidating the genetic diversity, relationships, and population structure analysis in RJF and domestic chicken populations.     

Comparison of SSR and SNP Markers in Estimation of Genetic Diversity and Population Structure of Indian Rice Varieties

Simple sequence repeat (SSR) and Single Nucleotide Polymorphic (SNP), the two most robust markers for identifying rice varieties were compared for assessment of genetic diversity and population structure. Total 375 varieties of rice from various regions of India archived at the Indian National GeneBank, NBPGR, New Delhi, were analyzed using thirty six genetic markers, each of hypervariable SSR (HvSSR) and SNP which were distributed across 12 rice chromosomes. A total of 80 alleles were amplified with the SSR markers with an average of 2.22 alleles per locus whereas, 72 alleles were amplified with SNP markers. Polymorphic information content (PIC) values for HvSSR ranged from 0.04 to 0.5 with an average of 0.25. In the case of SNP markers, PIC values ranged from 0.03 to 0.37 with an average of 0.23. Genetic relatedness among the varieties was studied; utilizing an unrooted tree all the genotypes were grouped into three major clusters with both SSR and SNP markers. Analysis of molecular variance (AMOVA) indicated that maximum diversity was partitioned between and within individual level but not between populations. Principal coordinate analysis (PCoA) with SSR markers showed that genotypes were uniformly distributed across the two axes with 13.33% of cumulative variation whereas, in case of SNP markers varieties were grouped into three broad groups across two axes with 45.20% of cumulative variation. Population structure were tested using K values from 1 to 20, but there was no clear population structure, therefore Ln(PD) derived Δk was plotted against the K to determine the number of populations. In case of SSR maximum Δk was at K=5 whereas, in case of SNP maximum Δk was found at K=15, suggesting that resolution of population was higher with SNP markers, but SSR were more efficient for diversity analysis.     

内蒙古西伯利亚杏群体遗传多样性和遗传结构分析

利用27对SSR分子标记对内蒙古地区13个西伯利亚杏群体的遗传多样性和遗传结构进行分析,评价其遗传多样性水平和分化程度,为内蒙古西伯利亚杏资源的合理保护与利用提供理论依据。结果显示:(1)27对SSR引物共检测到512个等位基因(Na),各位点平均等位基因数(Na)和多态性信息含量(PIC)分别为19和0.84;物种水平上Shannons信息指数(I)和期望杂合度(He)分别为2.25和0.73。(2)群体水平上的等位基因(Na)、有效等位基因(Ne)、Shannons信息指数(I)、期望杂合度(He)和观察杂合度(Ho)分别为6.95、4.48、1.60、0.76和0.56;其中科左后旗群体遗传多样性最丰富,克什克腾旗群体遗传多样性最低。(3)基于F统计量分析的遗传分化系数(Fst)为0.12,基因流(Nm)为1.86;分子方差分析显示内蒙古西伯利亚杏群体大部分遗传变异来自群体内(92%),群体间的遗传变异仅占8%。(4)内蒙古西伯利亚杏群体遗传距离为0.04~0.67,遗传相似度为0.33~0.83;遗传相似度的聚类分析、遗传距离的主坐标分析和遗传结构分析(Structure)均将供试13个群体划分为4组。Mantel检测显示,内蒙古西伯利亚杏群体遗传距离与地理距离呈显著相关关系(r=0.453,P0.01)。研究表明,内蒙古西伯利亚杏资源具有丰富的遗传多样性,这一特性与其群体的大小、悠久的演化历史以及自身生物学特性相关;内蒙古西伯利亚杏群体间存在中等程度的遗传分化,这可能源于自然地理隔离以及近期人类活动引起的生境片段化。     

Genetic Variation within Native Populations of Endemic Silkmoth Antheraea assamensis (Helfer) from Northeast India Indicates Need for In Situ Conservation

A. assamensis is a phytophagous Lepidoptera from Northeast India reared on host trees of Lauraceae family for its characteristic cocoon silk. Source of these cocoons are domesticated farm stocks that crash frequently and/or wild insect populations that provide new cultures. The need to reduce dependence on wild populations for cocoons necessitates assessment of genetic diversity in cultivated and wild populations. Molecular markers based on PCR of Inter-simple sequence repeats (ISSR) and simple sequence repeats (SSR) were used with four populations of wild insects and eleven populations of cultivated insects. Wild populations had high genetic diversity estimates (H_i = 0.25; H_S = 0.28; H_E = 0.42) and at least one population contained private alleles. Both marker systems indicated that genetic variability within populations examined was significantly high. Among cultivated populations, insects of the Upper Assam region (H_i = 0.19; H_S = 0.18; H_E = 0) were genetically distinct (F _ST = 0.38 with both marker systems) from insects of Lower Assam (H_i = 0.24; H_S = 0.25; H_E = 0.3). Sequencing of polymorphic amplicons suggested transposition as a mechanism for maintaining genomic diversity. Implications for conservation of native populations in the wild and preserving in-farm diversity are discussed.     

Genetic Diversity and Population Structure of the Brachiaria brizantha Germplasm

Brachiaria brizantha (Hochst. ex A. Rich.) Stapf. (syn. Urochloa brizantha (Hochst. ex A. Rich.) R.D. Webster) is a species used primarily as forage in tropical America and Southeast Asia. B. brizantha has been extensively researched since the 1980s with the initiation of the Tropical Forages Breeding Program conducted by the Brazilian Agricultural Research Corporation (Empresa Brasileira de Pesquisa Agropecuária; EMBRAPA), holding one of the largest germplasm collections in the world. This work has identified 15 new microsatellite markers for this species, which have been used in addition to five previously reported markers, to estimate the genetic similarities among 172 accessions and six cultivars of this species. Similarity index values ranged from 0.40 to 1.00. Two duplications were found in the germplasm. A Bayesian analysis performed using the STRUCTURE 2.3.3 program revealed the presence of three clusters with different allelic pools. This analysis is valuable for the performance of crosses to explore heterosis; however, the mode of reproduction of the accessions and ploidy barriers must be observed for effective exploration. A grouping analysis using the neighbor-joining method was consistent with the STRUCTURE analysis, and a combination approach suggested that this germplasm collection does not exhibit considerable genetic variability despite the presence of three distinct allelic pools. The lack of correlation between the genetic and geographic distances is also discussed.     

Genetic Diversity and Population Structure of Theileria annulata in Oman

Background

Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle.

Methods

Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites) representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman.

Results

We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia). A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise F_ST values being less than 0.03. Slightly higher F_ST values (G_ST’ = 0.075, θ = 0.07) were detected when the data for T. annulata parasites in Oman was compared with that previously generated for Turkey and Tunisia.

Conclusion

Genetic analyses of T. annulata samples representing four geographical regions in Oman revealed a high level of genetic diversity in the parasite population. There was little evidence of genetic differentiation between parasites from different regions, and a high level of genetic diversity was maintained within each sub-population. These findings are consistent with a high parasite transmission rate and frequent movement of animals between different regions in Oman.